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Crystal structure of C-terminal domain of precorrin-6Y C5,15-methyltransferase from Rhodobacter capsulatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HM2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 292 0.1M tri-sodium citrate dihydrate pH 5.6, 20% isopropanol and 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.12 42.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.354 α = 90 b = 44.799 β = 119.75 c = 84.11 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2008-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.011 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.7 72.93 99.9 0.06 0.06 14.6 3.6 10412 10402
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 100 0.214 0.214 5.3 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HM2 2.7 40.54 9909 9897 499 99.88 0.18868 0.18493 0.1828 0.26483 0.264 RANDOM 38.688
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.554 r_dihedral_angle_4_deg 21.261 r_dihedral_angle_3_deg 19.214 r_dihedral_angle_1_deg 7.086 r_scangle_it 3.1 r_scbond_it 1.804 r_angle_refined_deg 1.606 r_mcangle_it 1.233 r_mcbond_it 0.641 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.554 r_dihedral_angle_4_deg 21.261 r_dihedral_angle_3_deg 19.214 r_dihedral_angle_1_deg 7.086 r_scangle_it 3.1 r_scbond_it 1.804 r_angle_refined_deg 1.606 r_mcangle_it 1.233 r_mcbond_it 0.641 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2790 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 77
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling